title: MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action.
abstract: Microarray expression analyses following miRNA transfection/inhibition and, more recently, Argonaute cross-linked immunoprecipitation (CLIP)-seq assays have been used to detect miRNA target sites. CLIP and expression approaches measure differing stages of miRNA functioning-initial binding of the miRNP complex and subsequent message repression. We use nonparametric predictive models to characterize a large number of known target and flanking features, utilizing miRNA transfection, HITS-CLIP, and PAR-CLIP data. In particular, we utilize the precise spatial information provided by CLIP-seq to analyze the predictive effect of target flanking features. We observe distinct target determinants between expression-based and CLIP-based data. Target flanking features such as flanking region conservation are an important AGO-binding determinant-we hypothesize that CLIP experiments have a preference for strongly bound miRNP-target interactions involving adjacent RNA-binding proteins that increase the strength of cross-linking. In contrast, seed-related features are major determinants in expression-based studies, but less so for CLIP-seq studies, and increased miRNA concentrations typical of transfection studies contribute to this difference. While there is a good overlap between miRNA targets detected by miRNA transfection and CLIP-seq, the detection of CLIP-seq targets is largely independent of the level of subsequent mRNA degradation. Also, models built using CLIP-seq data show strong predictive power between independent CLIP-seq data sets, but are not strongly predictive for expression change. Similarly, models built from expression data are not strongly predictive for CLIP-seq data sets, supporting the finding that the determinants of miRNA binding and mRNA degradation differ. Predictive models and results are available at http://servers.binf.ku.dk/antar/.
authors.affiliation: The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.
authors.forename: Jiayu
authors.initials: J
authors.lastname: Wen
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Parker
authors.forename: Anders
authors.initials: A
authors.lastname: Jacobsen
authors.forename: Anders
authors.initials: A
authors.lastname: Krogh
mesh_terms: D020413:3' Untranslated Regions; D057809:HEK293 Cells; D006801:Humans; D047468:Immunoprecipitation / Q000379:methods*; D020407:Internet; D035683:MicroRNAs / Q000032:analysis* / Q000235:genetics; D019076:Transgenes
chemical_list: D020413:3' Untranslated Regions; D035683:MicroRNAs